Environmental bio-monitoring with high-throughput sequencing.

There is much interest in using high-throughput DNA sequencing methodology to monitor microorganisms, complex plant and animal communities. However, there are experimental and analytical issues to consider before applying a sequencing technology, which was originally developed for genome projects, to ecological projects. Many of these issues have been highlighted by recent microbial studies. Understanding how high-throughput sequencing is best implemented is important for the interpretation of recent results and the success of future applications. Addressing complex biological questions with metagenomics requires the interaction of researchers who bring different skill sets to problem solving. Educators can help by nurturing a collaborative interdisciplinary approach to genome science, which is essential for effective problem solving. Educators are in a position to help students, teachers, the public and policy makers interpret the new knowledge that metagenomics brings. To do this, they need to understand, not only the excitement of the science but also the pitfalls and shortcomings of methodology and research designs. We review these issues and some of the research directions that are helping to move the field forward.

Detection and diversity of pathogenic Vibrio from Fiji.

Here we investigate the diversity of pathogenic Vibrio species in marine environments close to Suva, Fiji. We use four distinct yet complementary analyses - biochemical testing, phylogenetic analyses, metagenomic analyses and molecular typing - to provide some preliminary insights into the diversity of vibrios in this region. Taken together our analyses confirmed the presence of nine Vibrio species, including three of the most important disease-causing vibrios (i.e. V. cholerae, V. parahaemolyticus and V. vulnificus), in Fijian marine environments. Furthermore, since toxigenic V. parahaemolyticus are present on fish for consumption we suggest these bacteria represent a potential public health risk. Our results from Illumina short read sequencing are encouraging in the context of microbial profiling and biomonitoring. They suggest this approach may offer an efficient and cost-effective method for studying the dynamics of microbial diversity in marine environments over time.

Isolation and characterization of aerobic thermophilic bacteria from the savusavu hot springs in fiji.

The relative isolation and unique physical properties of the Savusavu Hot Springs in Fiji may yield unique thermophiles. This study was conducted to determine the presence of aerobic thermophilic bacteria in these hot springs. A total of 104 thermophilic bacterial isolates were characterized and using Thermus and Bacillus strains as controls, 58% of the isolates were identified as Anoxybacillus flavithermus, 19% as Geobacillus stearothermophilus/Bacillus licheniformis, 10% as Thermus sp. TG153 and 10% as Thermus sp. TG206. Four isolates were unique in their molecular patterns suggesting there may be novel bacteria in the Savusavu hot springs.